Contacts of the strand formed by residues 258 - 262 (chain C) in PDB entry 6B5G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ILE* 4.1 20.9 - - + -
179C VAL 3.5 1.6 + - - -
180C CYS* 3.4 20.4 - - + -
181C GLY 2.7 31.4 + - - -
256C ILE* 3.3 6.8 - - - +
257C ASP* 1.3 81.5 - - - +
259C ILE* 1.3 73.1 + - - +
260C ALA* 4.0 5.4 - - - +
281C LYS* 4.1 2.0 - - - +
282C ARG* 3.3 19.6 - - + +
283C VAL 4.3 1.2 - - - -
284C THR* 3.0 32.7 + - - +
502C GLU* 3.6 15.6 + - - +
503C TYR* 3.4 42.6 - - + -
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Residues in contact with ILE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLY* 3.1 7.9 - - - +
183C ILE* 3.8 18.4 - - + -
250C ILE* 3.8 27.6 - - + -
251C ALA* 3.8 22.4 - - + -
256C ILE* 5.4 0.4 - - + -
258C LYS* 1.3 79.1 + - - +
260C ALA* 1.3 69.9 + - - +
261C PHE* 4.5 1.8 - - + +
271C ILE* 4.1 16.6 - - + -
275C ALA* 4.9 1.1 - - + -
281C LYS* 3.9 16.8 - - + -
282C ARG 2.8 18.6 + - - +
283C VAL* 3.3 26.3 - - + -
284C THR 2.9 25.1 + - - +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C GLY 2.9 6.1 + - - -
182C GLN* 3.3 8.8 - - + -
183C ILE 3.1 23.2 + - - -
196C LYS* 3.4 20.3 + - + +
258C LYS* 4.0 12.9 - - - +
259C ILE* 1.3 73.8 - - - +
261C PHE* 1.3 60.0 + - - +
284C THR* 3.6 10.3 - - + -
494C GLU* 4.7 3.6 - - - +
503C TYR* 3.3 26.7 - - - +
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Residues in contact with PHE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ILE* 3.6 20.0 - - + +
196C LYS* 3.6 0.4 - - - -
259C ILE* 4.0 4.7 - - + -
260C ALA* 1.3 72.4 - - - +
262C THR* 1.3 67.6 + - - +
263C GLY* 3.4 30.7 - - - -
264C SER 3.7 13.5 - - - -
267C VAL* 3.7 26.2 - - + -
268C GLY* 3.8 7.4 - - - -
271C ILE* 3.9 24.0 - - + -
284C THR* 3.0 8.4 + - - +
285C LEU* 3.5 21.0 - - + -
286C GLU* 2.9 25.5 + - - +
287C LEU* 3.7 15.5 - - + -
494C GLU* 5.5 0.6 + - - +
601C NAD 3.1 30.1 - - - -
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Residues in contact with THR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ILE 2.9 12.4 + - - +
184C ILE* 3.8 1.8 - - - -
185C PRO* 3.2 32.5 - - + +
192C MET* 3.9 8.5 - - - -
196C LYS* 2.6 32.0 + - - +
261C PHE* 1.3 83.2 + - - +
263C GLY* 1.3 58.6 + - - +
286C GLU* 3.3 11.5 - - - +
494C GLU* 3.9 3.5 + - - -
601C NAD 3.4 49.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il